Project description:Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets. Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR. DNA amplicons were sequenced using an Ilumina Genome Analyzer. Resulting sequences were computationally trimmed to remove 3' adaptor sequences. Raw data files (fastq) are unavailable for two of the samples (A.lyrata_flowers-stage1-12_rep1 and A.lyrata_flowers-stage1-12_rep2).
Project description:Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets.
Project description:Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets.
Project description:Environmental stresses trigger distinct responses between stress-sensitive and stress-adapted plants. To explore these stress adaptations at the cellular level, we built root single-cell transcriptome atlases for five biodiverse Brassicaceae species, including two stress-sensitive models (Arabidopsis thaliana and Sisymbrium irio), two extremophytes (Eutrema salsugineum and Schrenkiella parvula), and a polyploid oil crop (Camelina sativa), under control, salt, and ABA treatments. Although these species share similar root anatomy, most Arabidopsis cell type markers were not conserved across species. Cortex cell populations with distinct transcriptomes were spatially segregated among species. Lineage-specific gains in stress responses were more common than losses among cell-type responses across species. The homeologs in the allohexaploid C. sativa showed stress response divergence that was often decoupled from the divergence in their coding sequences and control expression levels. Our dataset provides a foundational root atlas across multiple Brassicaceae species enhanced for user accessibility with a cross species searchable browser and provides an analytical framework for comparative single-cell transcriptomics that can be readily transferred to any multi-species system.
